[BUG] MSIX build: mcpServers config never invoked, and "Install Unpacked Extension" fails with "Extension not found" — both local-MCP paths broken

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Environment:

• Claude Desktop version: 1.24012.9 (03c61d) — confirmed current latest release
• Install type: MSIX/Microsoft Store (package: Claude_pzs8sxrjxfjjc)
• OS: Windows 11, build 10.0.26200, standalone/unmanaged device (confirmed via dsregcmd /status and gpresult /r — no domain join, no GPOs, no MDM enrollment)
• Claude account: Free/personal

Summary:
Both supported methods for adding a local MCP server fail, with distinct symptoms, on this MSIX build.

Path 1 — Manual mcpServers config:

1. Added a valid entry to %APPDATA%\Claude\claude_desktop_config.json:

"mcpServers": {
  "github": {
    "command": "C:\\mcp-servers\\github-mcp-server.exe",
    "args": ["stdio"],
    "env": { "GITHUB_PERSONAL_ACCESS_TOKEN": "<redacted>" }
  }
}

1. Confirmed valid JSON via ConvertFrom-Json — parses cleanly, contains the block
2. Confirmed the binary works correctly standalone (clean startup/connect logs via & github-mcp-server.exe stdio)
3. Confirmed via MCP Inspector (npx @modelcontextprotocol/inspector) that the same command/args/env connects successfully and lists tools — server is fully functional over stdio/MCP protocol
4. After a full restart (verified via Task Manager that no Claude.exe process persisted), the server is never launched: github-mcp-server.exe never appears in Task Manager (watched in real time across multiple restarts), no mcp-server-*.log is ever created in %APPDATA%\Claude\logs\, and re-querying (Get-Content ... | ConvertFrom-Json).mcpServers after restart returns empty despite the raw file still containing the block

Path 2 — Install Unpacked Extension:

1. Built a minimal valid manifest per the current MCPB spec (manifest_version: 0.3, required author field included, server.type: binary)
2. Confirmed manifest parses cleanly via ConvertFrom-Json
3. Settings → Extensions → Advanced Settings → Install Unpacked Extension → selected the folder
4. Install fails immediately with "Extension not found"
5. Ruled out: MSIX sandbox folder-location restriction (moved folder into Documents, same result), disk space (~72GB free), file permissions (icacls shows standard ACL, no restriction for the user account)

Also ruled out as contributing factors:

• MSIX "wrong config file" bug — searched the entire %LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\ tree recursively (including full-text search for mcpServers across all .json files) — no secondary config file exists anywhere
• Device management / MDM (isLocalDevMcpEnabled) — device confirmed unmanaged

Expected behavior: Either path should result in the GitHub MCP server launching and its tools appearing via the hammer/tools icon.

Actual behavior: Path 1 — zero launch attempt, zero logs, ever. Path 2 — install fails outright with "Extension not found."

Possibly related:

• #67843 (MSIX filesystem virtualization failure during extension install)
• #67839 (extension installs silently failing on a specific MSIX build)
• #67919 (uninstalled extension can't be reinstalled, MSIX-specific)
• modelcontextprotocol/mcpb#281 (MSIX-specific .mcpb install regression, same package ID Claude_pzs8sxrjxfjjc)

Version differs from those reports (1.24012.9 vs. their cited builds), so this may be a related-but-distinct MSIX regression rather than the identical bug — flagging for whoever triages to confirm.

What Should Happen?

1. Config or extension installed → Claude Desktop launches github-mcp-server.exe as a background process automatically on startup
2. Hammer/tools icon appears in the chat interface, showing "github" as a connected MCP server
3. You ask me something like "list branches for Andre-sdk/AngleMasterV4" or "show me open issues in that repo"
4. I see GitHub tools available (things like list_branches, get_file_contents, list_issues, search_code, etc.) and call them directly
5. Results come back — actual branch names, file contents, issue lists — pulled live from your repo via your PAT's permissions, no copy-pasting needed on my end.

Error Messages/Logs

Steps to Reproduce

Steps to Reproduce

Path 1 — Manual config:

1. Open Claude Desktop → Settings → Developer → Edit Config
2. Add the following to mcpServers in claude_desktop_config.json:

``json
"mcpServers": {
"github": {
"command": "C:\\mcp-servers\\github-mcp-server.exe",
"args": ["stdio"],
"env": { "GITHUB_PERSONAL_ACCESS_TOKEN": "<token>" }
}
}
``

1. Save the file
2. Fully quit Claude Desktop (confirm via Task Manager that no Claude.exe process remains)
3. Relaunch Claude Desktop
4. Observe: no hammer/tools icon appears; github-mcp-server.exe never appears in Task Manager; no mcp-server-github.log is created in %APPDATA%\Claude\logs\

Path 2 — Install Unpacked Extension:

1. Create a folder containing github-mcp-server.exe and a manifest.json conforming to MCPB spec v0.3 (binary server type, required author field included)
2. In Claude Desktop: Settings → Extensions → Advanced Settings → Install Unpacked Extension
3. Select the folder in the picker
4. Observe: install immediately fails with "Extension not found"

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

n/a

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_